PDB record fields¶
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namespace mdk
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namespace pdb
Enums
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enum Mode
A mode enum, which modifies how to position and parse strings. Note: most enums in the program are enum classes; here we need a standard enum in order for combining via
| to workValues:
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enumerator Exact
Beginning of the field in the line. Inclusive and 1-indexed, as in the PDB format docs, in order to make writing new fields easier.
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enumerator Trim
When parsing, the final value is a trimmed string read from the line.
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enumerator Left
When writing, the string is written left-aligned in the line.
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enumerator Right
When writing, the string is written right-aligned in the line.
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enumerator Exact
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class Field
- #include <Field.hpp>
An object representing a single field of a PDB record, along with the means of parsing and printing it. The field objects signal parsing failure by throwing.
Subclassed by mdk::pdb::Char, mdk::pdb::Integer, mdk::pdb::Literal, mdk::pdb::Real, mdk::pdb::String, mdk::pdb::SymOp
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class Integer : public mdk::pdb::Field
- #include <Field.hpp>
Integer field.
Public Functions
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inline Integer(int i, int j, int &v, int offset = 0)
Private Members
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int i
Beginning of the field in the line. Inclusive and 1-indexed, as in the PDB format docs, in order to make writing new fields easier.
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int j
End of the field in the line. Inclusive and 1-indexed, as in the PDB format docs, in order to make writing new fields easier.
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int offset
A value that is added to the read value and subtracted when a value is written. It’s chiefly used to convert 0-indexed ordinals to 1-indexed and vice versa.
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int *v
A pointer to the integer to save the value to and load the value from. It allows us in particular to have the same field class for many different PDB records, only having to provide different pointer to the underlying value.
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inline Integer(int i, int j, int &v, int offset = 0)
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class Real : public mdk::pdb::Field
- #include <Field.hpp>
Real (floating number) field.
Public Functions
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inline Real(int i, int j, int n, int m, double &v, double scalar = 1.0)
Private Members
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int i
Beginning of the field in the line. Inclusive and 1-indexed, as in the PDB format docs, in order to make writing new fields easier.
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int j
End of the field in the line. Inclusive and 1-indexed, as in the PDB format docs, in order to make writing new fields easier.
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int n
Width of the read real number. Follows the conventions from the PDB format docs and Fortran specifiers (it’s n in f{n}.{m})
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int m
Precision of the read real number. Follows the conventions from the PDB format docs and Fortran specifiers (it’s m in f{n}.{m})
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double *v
A pointer to the double to save the value to and load the value from. It allows us in particular to have the same field class for many different PDB records, only having to provide different pointer to the underlying value.
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double scalar
Scalar by which to multiply a read value and divide a written value. In particular, it allows us to convert PDB file formats to internal units and back.
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inline Real(int i, int j, int n, int m, double &v, double scalar = 1.0)
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class String : public mdk::pdb::Field
- #include <Field.hpp>
String field. By default read values are trimmed, and written values are right-aligned.
Public Functions
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inline String(int i, int j, std::string &v, int8_t mode = Trim | Right)
Private Members
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int i
Beginning of the field in the line. Inclusive and 1-indexed, as in the PDB format docs, in order to make writing new fields easier.
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int j
End of the field in the line. Inclusive and 1-indexed, as in the PDB format docs, in order to make writing new fields easier.
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std::string *v
A pointer to the string to save the value to and load the value from. It allows us in particular to have the same field class for many different PDB records, only having to provide different pointer to the underlying value.
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int8_t mode
Mode of string parsing and writing. See
Modefor details.
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inline String(int i, int j, std::string &v, int8_t mode = Trim | Right)
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class Char : public mdk::pdb::Field
- #include <Field.hpp>
(Single) character field.
Public Functions
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inline Char(int i, char &v)
Private Members
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int i
The location of the character in the line. Inclusive and 1-indexed, as in the PDB format docs, in order to make writing new fields easier.
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char *v
A pointer to the character to save the value to and load the value from. It allows us in particular to have the same field class for many different PDB records, only having to provide different pointer to the underlying value.
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inline Char(int i, char &v)
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class SymOp : public mdk::pdb::Field
- #include <Field.hpp>
“Symmetry operator” field. At the moment it’s parsed just like a normal string.
Public Functions
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inline SymOp(int i, int j, std::string &v)
Private Members
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int i
Beginning of the field in the line. Inclusive and 1-indexed, as in the PDB format docs, in order to make writing new fields easier.
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int j
End of the field in the line. Inclusive and 1-indexed, as in the PDB format docs, in order to make writing new fields easier.
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std::string *v
A pointer to the string to save the value to and load the value from. It allows us in particular to have the same field class for many different PDB records, only having to provide different pointer to the underlying value.
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inline SymOp(int i, int j, std::string &v)
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class Literal : public mdk::pdb::Field
- #include <Field.hpp>
A literal. As opposed to a normal field, here there’s no reading or writing values by pointers, rather comparing the read value with the literal and printing out the literal. It’s chiefly used for parsing the record headers, like “ATOM ” or “MODEL “.
Public Functions
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inline Literal(int i, int j, std::string lit)
Private Members
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int i
Beginning of the field in the line. Inclusive and 1-indexed, as in the PDB format docs, in order to make writing new fields easier.
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int j
End of the field in the line. Inclusive and 1-indexed, as in the PDB format docs, in order to make writing new fields easier.
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inline Literal(int i, int j, std::string lit)
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enum Mode
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namespace pdb